Biology Reference
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determines much of the behaviour of each individual molecule. In biology, this
part of the molecule's behaviour often leads to important function. An example
of the molecular behaviour that only originates in the dynamic interactions with
the other molecules, is found with the molecules that are 'responsible for' the
cell cycle. None of these would have a cyclic activity in the absence of the
others, and this collective cycling is assumed to be the only biological function
of these molecules.
The ultimate silicon-cell strategy completely recovers the emergence of func-
tional behaviour of molecules from this resonating with the other molecules.
A completely reductionistic approach would look only at the behaviour of the
individual molecules, perhaps in an environment that is a frozen representation
of the molecules' environment in the living organism. It then sees the behaviour
of the living organism as the sum of these molecular behaviours, and thereby
misses the extra molecular behaviour that stems from the cycle of interactions
running through the other molecules. It would not comprehend the cell cycle, as
it would perhaps observe but not explain the cycling.
An important issue is whether the silicon cell requires only molecular knowl-
edge or also systems knowledge to start from. For sure, it does not require
systems knowledge of the resonating type (cf. above). On the other hand, the
systems of interest are nonlinear and the response of the molecules to the changes
in their immediate environment do depend on the average state around which
these changes occur, such as intracellular pH and ionic strength. The latter are
indeed established by the system as a whole, and in this sense systems properties
that correspond to the static physiological state do enter the silicon-cell models.
These properties are static in the sense that they could be determined by taking
a photograph (Kell and Mendes, 2000), or when they are time dependent, by
a movie of the system around the macromolecule of interest. These properties
are essentially parameters for the functioning of the interacting macromolecules,
whereas the properties that create emergent properties are dynamic variables
(cf. below).
As in fundamental physics, there could be cases where it is not really possi-
ble to consider macromolecules separately from their molecular environments.
In these cases, their complete environment is codetermined by the dynamic
behaviour of the macromolecules of interest. Then also, that entire environment
consists of variables that are influenced by the macromolecules under study.
This might (but would not have to) happen with regards to amino-acid residues
in the system of the surrounding amino acids in a protein, or in MAP kinase
cascades when all the kinases and phosphatases form a supercomplex, a scaffold.
The silicon-cell approach assumes that there is substantial possibility to con-
sider macromolecules separately from their environments. In cases where parts of
that immediate environment is not separable, that part needs to be taken together
with the macromolecule. This then still does not incapacitate the silicon-cell
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